Structure of PDB 7r7j Chain B Binding Site BS01

Receptor Information
>7r7j Chain B (length=574) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IFTLRPYQQEAVDATLNHFRRHKTPAVIVLPTGAGKSLVIAELARLARGR
VLVLAHVKELVAQNHAKYQALGLEADIFAAGLKRKESHGKVVFGSVQSVA
RNLDAFQGEFSLLIVDECHRIGDDEESQYQQILTHLTKVNPHLRLLGLTA
TPFRLGKGWIYQFHYHGMVRGDEKALFRDCIYELPLRYMIKHGYLTPPER
LDMPVVQYDFSRLQAQSNGLFSEADLNRELKKQQRITPHIISQIMEFAAT
RKGVMIFAATVEHAKEIVGLLPAEDAALITGDTPGAERDVLIENFFRYLV
NVAVLTTGFDAPHVDLIAILRPTESVSLYQQIVGRGLRLAPGKTDCLILD
YAGNPHDLYAPEVGTPKGKSDNVPVQVFCPACGFANTFWGKTTADGTLIE
HFGRRCQGWFEDDDGHREQCDFRFRFKNCPQCNAENDIAARRCRECDTVL
VDPDDMLKAALRLKDALVLRCSGMSLQHGHDEKGEWLKITYYDEDGADVS
ERFRLQTPAQRTAFEQLFIRPHTRTPGIPLRWITAADILAQQALLRHPDF
VVARMKGQYWQVREKVFDYEGRFR
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain7r7j Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7r7j X-ray crystal structure of the Escherichia coli RadD DNA repair protein bound to ADP reveals a novel zinc ribbon domain.
Resolution2.03 Å
Binding residue
(original residue number in PDB)		F3 R6 Q9 G34 A35 G36 K37 L39 K68 R343
Binding residue
(residue number reindexed from 1)		F2 R5 Q8 G33 A34 G35 K36 L38 K67 R338
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.12: DNA helicase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003697 single-stranded DNA binding
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0046872 metal ion binding
Biological Process
GO:0006281 DNA repair
GO:0006301 postreplication repair
GO:0006302 double-strand break repair
GO:0006412 translation
GO:0009410 response to xenobiotic stimulus
GO:0010212 response to ionizing radiation
GO:0051301 cell division

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7r7j, PDBe:7r7j, PDBj:7r7j
PDBsum7r7j
PubMed35482735
UniProtP33919|RADD_ECOLI Putative DNA repair helicase RadD (Gene Name=radD)

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